Net Pay calculation issue when you enter a PREPAY refund as a onetime deduction

We are having a Net Pay calculation issue with PREPAY refunds. We had six (6) employees last month where the Net Pay on the check was not equal to the expected / manually calculated net pay amount (Gross Pay - EE Deductions - EE Tax) Net pay on check was higher. We did not see any payroll error messages other than the "Earnings Went Negative" warnings we often see this time of year. But after they were confirmed if you look at the check they don't add up.

We ran the GL Interface, after the PAYGL02 process completed, the log file contained the following message for the six employees - "ERROR-Deductions on Paycheck does not match Employee Deductions for PAYCHECK_NBR". The journal was also out of balance on the GL side. We had some system generated PREPAY refunds that seemed to have worked fine but any PREPAY refunds entered as a one time deduction are having issues.